Dear All,
I would like to circulate some current Cheminformatics- (and related) news to everyone as follows – in particular, our next Cambridge Cheminformatics Meeting will take place on 23 April (Wednesday next week), as usual in hybrid mode at the CCDC and on Zoom, for details please see below.
So here we go …
Events
23 April 2025
Cambridge Cheminformatics Meeting
Hybrid Event (at the CCDC, Cambridge/on Zoom)
Direct Zoom registration:
https://cam-ac-uk.zoom.us/meeting/register/0tDTxqn-ROCoOUqI2Cq5HQ
More information on event series: https://www.c-inf.net
Programme
A Day in the Life of a Chief Data Science Officer: Making Data-Driven Decisions in Drug Discovery
Layla Hosseini-Gerami, Ignota Labs
https://www.ignotalabs.ai
Targeting the Unknown: Flagging High-Risk Chemicals in Environmental Samples Without Full Identification Using Machine Learning
Ida Rahu, University of Stockholm
https://www.linkedin.com/in/idarahu
Narrowing the Gap Between Machine Learning Scoring Functions and Free Energy Perturbation Using Augmented Data
Isak Valsson, Oxford University
www.linkedin.com/in/isak-valsson
… as usual, followed by a social, both in person and online. Please join us, and circulate further!
28 April 2025
International Helmholtz Drug Discovery Conference
Berlin, Germany
https://www.mdc-berlin.de/HDDC2025
28 May 2025
BMCS Hot Topics: PROTACs and Glues 2025
Virtual Event
https://www.rscbmcs.org/events/hottopicsprotacsandglues2025
18 June 2025
Persistent Challenges in Cheminformatics
London, UK
https://www.pistoiaalliance.org/eventdetails/persistent-challenges-in-cheminformatics
30 June 2025
Milner Therapeutics Symposium 2025
Cambridge, UK (and online, hybrid mode)
https://milner.glueup.com/event/milner-therapeutics-symposium-2025-132179
8-10 September 2025
Quantum Chemistry for Drug Design: From Theory to Applications
Prague, Czech Republic
https://www.cecam.org/workshop-details/quantum-chemistry-for-drug-design-from-theory-to-applications-1446
10-12 September 2025
RDKit UGM 2025 (Pre-Registration Open)
Prague, Czech Republic
https://docs.google.com/forms/d/e/1FAIpQLScsTXtKREl9XxFan4ZRWSMHLR-_-RgSC12_35-MmvXVILyv7g/viewform
11 September 2025
Workshop on AI in Drug Discovery (part of ICANN2025)
Kaunas, Lithuania
https://e-nns.org/icann2025/aidd
21-24 September 2025
Fragment-Based Lead Discovery Conference
Cambridge, UK
https://fbldconference.org
13/14 October 2025
PhysChem Forum 2025
Basel, Switzerland
http://www.physchem.org.uk
Jobs
(Senior) Computational Scientist, Machine Learning
Bind Research
London, UK
https://bindresearch.org/job-ml
Data Scientist, AI/ML Drug Discovery
Beerse, Belgium or other locations
https://www.careers.jnj.com/en/jobs/r-005362/data-scientist-aiml-drug-discovery
Research Scientist, Machine Learning
Isomorphic Labs
London, UK
https://job-boards.greenhouse.io/isomorphiclabs/jobs/5224363004?gh_src=6dd50a764us
Senior Specialist in Computational Toxicology
Nestle
Lausanne, Switzerland
https://www.linkedin.com/jobs/view/4160113871
Scientific Director Computational Chemistry
Boehringer Ingelheim
Vienna, Austria
https://www.linkedin.com/comm/jobs/view/4203429741
Max Planck Research Group Leader in Molecular Design
Max-Planck-Institute for Polymer Research
Mainz, Germany
https://www.linkedin.com/jobs/view/4199991803
Postdoctoral Research Fellow, AI-Enabled SBDD
University of Bergen
Bergen, Norway
https://www.jobbnorge.no/en/available-jobs/job/276846/lead-ai-postdoctoral-research-fellow-within-ai-enabled-structure-based-drug-design
Postdoctoral Fellow, Molecular Modelling
Babes-Bolyai University
Cluj, Romania
https://www.cojocarulab.eu/oportunities.html
Postdoctoral/PhD Research Position in Machine Learning for Molecular Mechanics
Max-Planck Institute for Polymer Research
Mainz, Germany
https://www.mpip-mainz.mpg.de/1000922/202502-ml-for-mm?c=944116
PhD Position – Mitigating Synthesisability Loss in 3D Generative Models
University of Liverpool
Liverpool, UK
https://www.liverpool.ac.uk/study/postgraduate-research/studentships/mitigating-synthesisability-loss-in-3d-generative-models
PhD Position in Machine Learning for Protein Structure Prediction
UCT Prague
Prague, Czech Republic
https://euraxess.ec.europa.eu/jobs/322881
PhD Position, Protein-Ligand Interaction Dynamics
Wageningen University
Wageningen, The Netherlands
https://www.linkedin.com/jobs/view/4203444687
PhD Position, Computational Drug Design
Universitaet Muenster
Muenster, Germany
https://stellen.uni-muenster.de/jobposting/5e706d77e7afaa3a4bd7c42e48748d9aacb38b2b0?ref=homepage
Cheminformatics…
Benchmarking chemical exploration in de novo drug design with MolExp
https://cheminformantics.blogspot.com/2025/02/benchmarking-chemical-exploration-in-de.html
Blog post by Morgan Thomas
Searching a local copy of PubChem
https://macinchem.org/2025/02/17/searching-a-local-copy-of-pubchem
Using DILIPred
https://macinchem.org/2025/03/02/using-dilipred/
Blog posts by Chris Swain
Conformal prediction-based machine learning in Cheminformatics: Current applications and new challenges
https://www.sciencedirect.com/science/article/pii/S2667318525000030
Nice review in the above area
PandaDock: Physics-Based Molecular Docking using Python
https://github.com/pritampanda15/PandaDock
‘PandaDock is a Python-based molecular docking tool that combines traditional docking approaches with advanced physics-based scoring and CHARMm-inspired algorithms’
3DP-Jmol
https://github.com/mariusmihasan/3DP-JMol/releases
‘3DP-Jmol is a Jmol-based script that automatically generates 3D printable molecular models from structural data’
Cambridge Cheminformatics Meeting, 19 February 2025 – Recording Online!
https://youtu.be/Hd_KuxXLCUg
De Novo Design of GPCR Ligands, Molecular Simulations for Force Fields, Gaussian Processes in Chemistry
First DREAM Target 2035 Drug Discovery Challenge
https://www.synapse.org/Synapse:syn65660836/wiki/631410
‘In this inaugural DREAM Target 2035 Challenge, we are inviting the community of data scientists to build Machine learning models based on molecular data from DNA encoded libraries (or DELs) to efficiently discover hits (bioactive drug-like molecules) ‘
A Gentle Introduction to Machine Learning for Chemists: An Undergraduate Workshop Using Python Notebooks for Visualization, Data Processing, Analysis, and Modeling
https://doi.org/10.1021/acs.jchemed.1c00142
Uni-pKa
https://github.com/dptech-corp/Uni-pKa?tab=readme-ov-file
‘The official implementation of the model Uni-pKa in the paper Bridging Machine Learning and Thermodynamics for Accurate pKa Prediction’
Introduction to Cheminformatics and AI in Drug Discovery: Hands-on Modeling of Safety Data
https://srijitseal.com/AIDDCourse
by Srijit Seal
Mychem
https://mychem.github.io
‘Mychem is a chemoinformatics extension for MySQL and MariaDB released under the GNU GPL license’
PLACER
https://github.com/baker-laboratory/PLACER
‘PLACER is graph neural network for local prediction of protein-ligand conformational ensembles’
Osmordred
https://www.linkedin.com/pulse/osmordred-guillaume-godin-qasme
‘a dedicated package for 0 to 2D molecular features (3586 so far), licensed under the BSD-3-Clause license, the same as RDKit’
Have protein-ligand co-folding methods moved beyond memorisation?
https://www.biorxiv.org/content/10.1101/2025.02.03.636309v1
Short answer: no (see article for more details)
Professor Graham Richards – RIP
https://www.bnc.ox.ac.uk/about-brasenose/news/2909-professor-graham-richards
Related:
1. Secrets from a spin-out success story
https://www.nature.com/articles/s41570-024-00634-x
2. Spin-out doctor
https://www.theguardian.com/education/2009/feb/10/graham-richards
3. From diatomics to drugs and dividends
https://www.sciencedirect.com/science/article/pii/S1093326307000733
OpenMMDL
https://github.com/wolberlab/OpenMMDL
‘Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes’
Biosynfoni: A Biosynthesis-informed and Interpretable Lightweight Molecular Fingerprint
https://chemrxiv.org/engage/chemrxiv/article-details/67a6c0426dde43c90801e335
For ‘biosynthetic distance estimation, using 39 substructural keys
Is Tanimoto a metric?
https://www.biorxiv.org/content/10.1101/2025.02.18.638904v1.full.pdf
Summary: no (a nice read for the weekend though)
… beyond Cheminformatics …
Introduction to Machine Learning
https://arxiv.org/abs/2409.02668
by Laurent Younes
Deep Impact
https://www.wheresyoured.at/deep-impact
‘In the last week or so, but especially over the weekend, the entire generative AI industry has been thrown into chaos’
My favourite paragraph: ‘The mythology of both OpenAI and Anthropic is that these large amounts of capital weren’t just necessary, but the only way to do this. While these companies ostensibly “compete,” neither of them seemed concerned about doing so as actual businesses that made products that were, say, cheaper and more efficient to run, because in doing so they would break the illusion that the only way to create “powerful artificial intelligence” was to hand billions of dollars to one of two companies, and build giant data centers to build even larger language models. ‘
How not to build an AI Institute
https://www.chalmermagne.com/p/how-not-to-build-an-ai-institute
‘What went wrong with the Alan Turing Institute?’
Optimal dietary patterns for healthy aging
https://www.nature.com/articles/s41591-025-03570-5
Fruit and veg, less meat.. some numbers to support the argument
Accelerating scientific breakthroughs with an AI co-scientist
https://research.google/blog/accelerating-scientific-breakthroughs-with-an-ai-co-scientist
My response: The ‘Google Co-Scientist’ Hasn’t (Yet) Lead to ‘Breakthroughs’ – A Closer Look at Its Scientific Validation
https://www.drugdiscovery.net/2025/02/20/the-google-co-scientist-hasnt-yet-lead-to-breakthroughs-a-closer-look-at-its-scientific-validation
A Neural Model of Attention, Reinforcement and Discrimination Learning
https://sites.bu.edu/steveg/files/2016/06/Gro1975IntRevNeurobiol.pdf
(from 1975; always good to put things into historical context)
A human metabolic map of pharmacological perturbations reveals drug modes of action
https://www.nature.com/articles/s41587-024-02524-5
China’s Low-Productivity Innovation Drive: Evidence from Patents
https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3714029
The Practical Guide to Biotech Partnerships
https://lucas-harrington.com/2025/02/13/the-practical-guide-to-biotech-partnerships
‘From First Date to Long-term Commitment: Lessons Learned from $200M of upfronts at Mammoth’
Evaluating student understanding of pharmacodynamics core concepts
https://www.sciencedirect.com/science/article/pii/S001429992500010X
What’s understood, what is not?
Leveraging Large-Scale Biobanks for Therapeutic Target Discovery
https://www.medrxiv.org/content/10.1101/2025.02.10.25321487v1
‘This model was able to accurately predict the odds of a particular significant MR (Mendelian Randomization) result being developed into an approved drug and its clinical indication (precision-recall AUC 0.79)’
AI Antibodies? Really?
https://www.science.org/content/blog-post/ai-antibodies-really
Comment by Derek Lowe
Scientists just rewrote our understanding of epigenetics
https://www.livescience.com/health/genetics/scientists-just-rewrote-our-understanding-of-epigenetics
Biology is, not too surprisingly, linked
Database: AI for (Life) Science Companies
https://thehardthing.notion.site/170aec01d7ce80b4a36bf499df793b41?v=170aec01d7ce8142939a000c41d4679c
… and clearly beyond Cheminformatics
Is asteroid 2024 YR4 going to hit Earth in 2032?
https://community.wolfram.com/groups/-/m/t/3389913
Probably not (i.e. with 2.3% Likelihood)
Exclusive: These universities have the most retracted scientific articles
https://www.nature.com/articles/d41586-025-00455-y
Related: Retraction Watch
https://retractionwatch.com
Can recommend a donation as well:
https://mailchi.mp/retractionwatch/resources-donate-15100471
Also related: Did a ‘nasty’ publishing scheme help an Indian dental school win high rankings?
https://www.science.org/content/article/did-nasty-publishing-scheme-help-indian-dental-school-win-high-rankings
‘Vegetative Electron Microscopy’
https://retractionwatch.com/2025/02/10/vegetative-electron-microscopy-fingerprint-paper-mill
Catch up in order not to miss this trend!
On Microsoft’s Majorana chip and the ‘Topological Qubit’…
https://www.linkedin.com/feed/update/urn:li:activity:7297965539937701888
See also: ‘This is a mega-thread of all Microsoft problems related to topological qubits’
https://bsky.app/profile/spinespresso.bsky.social/post/3likbu3x5lk2c
Periodic cooking of eggs
https://www.nature.com/articles/s44172-024-00334-w
‘Egg cooks are challenged by the two-phase structure: albumen and yolk require two cooking
temperatures’… ‘we are able to design the novel
cooking method, namely periodic cooking’ Finally!
Individual and additive effects of vitamin D, omega-3 and exercise on DNA methylation clocks of biological aging in older adults from the DO-HEALTH trial
https://www.nature.com/articles/s43587-024-00793-y
In short: it’s all good for you, now in numbers
AI Will Always Love You: Studying Implicit Biases in Romantic AI Companions
https://arxiv.org/abs/2502.20231
Somehow I feel I am getting too old for some of the current developments taking place on planet Earth
50 Years of Travel Tips
https://kk.org/thetechnium/50-years-of-travel-tips
Many I agree with … I am glad I travelled India before the times of Google Maps etc though
Elon Musk’s terrifying vision for AI
https://garymarcus.substack.com/p/elon-musks-terrifying-vision-for
by Gary Marcus
A replay of life: What happens in our brain when we die?
https://www.frontiersin.org/news/2022/02/22/what-happens-in-our-brain-when-we-die
‘When an 87-year-old patient developed epilepsy, Dr Raul Vicente of the University of Tartu, Estonia and colleagues used continuous electroencephalography (EEG) to detect the seizures and treat the patient. During these recordings, the patient had a heart attack and passed away. This unexpected event allowed the scientists to record the activity of a dying human brain for the first time ever’
I believe this is (nearly) all from my side for now – just one more personal item before I conclude: I have just moved to Abu Dhabi, where I am now a Professor for Machine Learning in Medicine / AI in Drug Discovery at Khalifa University. Please do let me know when you are in the area and happy to show you around!
And, as usual, if you have any information for me to circulate, or wish to present at one of our next Cambridge Cheminformatics Meetings, please just get in touch, cheers!
Best wishes,
Andreas